Cole Allen, 31, did not speak in court as his lawyer Tezira Abe entered the plea on his behalf.
The charges include attempted assassination of the president, assault on a federal officer and firearms offences.
Prosecutors allege Allen fired a shotgun at a US Secret Service agent and stormed a security checkpoint in a foiled attack on Trump and other members of his administration at the White House Correspondents' Dinner.
Allen allegedly travelled to Washington DC by train, carrying a shotgun, pistol and knives, and booked a room in the Washington Hilton where the April 25 dinner took place.
Allen wore an orange jumpsuit and was shackled at the waist during the brief court proceeding.
It was his first appearance in a Washington DC federal court before the judge who will preside over the remainder of the case, US District Judge Trevor McFadden.
The hearing came a week after a different judge apologised to Allen for his treatment in a local Washington DC jail, which included being placed on self-harm precautions and isolated from other inmates.
The proceeding previewed the next major legal battle in the case, Allen's attempt to have acting Attorney General Todd Blanche and US Attorney Jeanine Pirro disqualified from the case because they were present at the dinner and may have been among Allen's alleged targets.
Allen's lawyer Eugene Ohm said the defence is likely to seek recusal of the entire US Attorney's Office in Washington, which Pirro leads, because of her friendship with Trump and status as a potential victim.
"It is wholly inappropriate for victims of an alleged event like this to be individually prosecuting the case," Ohm said.
Prosecutors are set to respond to the defence's legal filing by May 22.
Pirro previously told CNN in an interview that "my ability to prosecute this case has nothing to do with my being there".
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